Reproducibility package for "Fishing bans yield trophic imbalance in impounded versus free-flowing waters"

This deposit is the integrated reproducibility package for the manuscript "Fishing bans yield trophic imbalance in impounded versus free-flowing waters" submitted to Nature Sustainability. It contains the input data, public reference inputs, corrected analysis code (Python and R), intermediate tables, and generated results needed to reproduce the analyses, figures, tables, and statistical claims in the paper.Contents========huang_djk_ns_reproducibility_v1.0.1.zip, provided as five split files:- huang_djk_ns_reproducibility_v1.0.1.zip.part01- huang_djk_ns_reproducibility_v1.0.1.zip.part02- huang_djk_ns_reproducibility_v1.0.1.zip.part03- huang_djk_ns_reproducibility_v1.0.1.zip.part04- huang_djk_ns_reproducibility_v1.0.1.zip.part05After concatenation, the archive contains:- RUN_ORDER.md: recommended execution order for the main manuscript and habitat-mechanism analyses- SOFTWARE_REQUIREMENTS.md: Python and R dependencies- NORMALIZED_SCRIPTS.txt: scripts normalized for relative-path execution- MANIFEST.csv: SHA256 inventory for the integrated archive- Source data: standardized fish surveys from Danjiangkou Reservoir (2021–2025, 21,996 individuals, 60 species), station coordinates, water-quality extracts, curated species-classification tables- Analysis code: Python and R scripts under report/NatSustain_submission/code/ and habitat_heterogeneity/scripts/- External reference inputs: Xiong et al. Yangtze fishing-ban data and derived CSV files required by the R scripts (Dryad doi:10.5061/dryad.wdbrv1635)- Public habitat/spatial inputs: JRC Global Surface Water (2021) raw GeoTIFFs, ESA WorldCover metadata, China province-level water-system shapefiles- Results: intermediate CSV/JSON/GPKG tables and generated PDF/PNG figures used to verify and reproduce the manuscript outputsHow to use==========cat huang_djk_ns_reproducibility_v1.0.1.zip.part* > huang_djk_ns_reproducibility_v1.0.1.zipshasum -a 256 huang_djk_ns_reproducibility_v1.0.1.zip# expected: ebc3fd94db28bd7ec642c52e2bbb0185080c5251533384238ec86ccf01f9803bunzip huang_djk_ns_reproducibility_v1.0.1.zipcd huang_djk_ns_reproducibility_v1.0.1# then follow RUN_ORDER.mdSystem requirements: Python 3.12 (pandas, numpy, scipy, statsmodels, matplotlib, openpyxl, geopandas, rasterio, shapely) and R 4.4 (readr, readxl, dplyr, tidyr, ggplot2, lme4, lmerTest).Data provenance===============- Danjiangkou Reservoir surveys: collected by the authors at 12 fixed stations in 2021–2025 under the Han (year-round ban since 2020-01) and Dan (seasonal ban, Mar–Aug) sub-basins.- Yangtze mainstem comparison data: archived from Xiong et al., Science (2026), Dryad doi:10.5061/dryad.wdbrv1635, redistributed here under the original CC0 licence for reproducibility.- JRC Global Surface Water (2021): public, Joint Research Centre.- ESA WorldCover and China province-level water-system shapefiles: public.Embargo=======This deposit is currently under embargo for peer review. It will be set to Open Access on the date of manuscript acceptance, or no later than 24 months from upload.Citation========If you use this package, please cite both the manuscript and this deposit (DOI assigned by Zenodo on upload).